Package org.biojava.bio.program.fastq

FASTQ and variants sequence format I/O.

To read from an Illumina variant FASTQ sequence file:

 FastqReader reader = new IlluminaFastqReader();
 for (Fastq fastq : reader.read(new File("illumina.fastq"))
 {
   // ...
 }
 

To write to an Sanger variant FASTQ sequence file:

 Collection<Fastq> fastq = ...;
 SangerFastqWriter writer = new SangerFastqWriter();
 writer.write(new File("sanger.fastq"), fastq);
 

For further documentation on the FASTQ sequence format, its variants, and how they are handled in O|B|F projects, see:

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
Nucleic Acids Research, doi:10.1093/nar/gkp1137

Since:

1.7.1

Interface Summary

Interface	Description
FastqReader	Reader for FASTQ formatted sequences.
FastqWriter	Writer for FASTQ formatted sequences.
ParseListener	Low-level event based parser callback.
StreamListener	Event based parser callback.

Class Summary

Class	Description
Fastq	FASTQ formatted sequence.
FastqBuilder	Fluent builder API for creating FASTQ formatted sequences.
FastqTools	Utility methods for FASTQ formatted sequences.
IlluminaFastqReader	Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter	Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
SangerFastqReader	Reader for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqWriter	Writer for FastqVariant.FASTQ_SANGER formatted sequences.
SolexaFastqReader	Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqWriter	Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.

Enum Summary

Enum	Description
FastqVariant	FASTQ sequence format variant.